. 2009 Apr 1;37(9):e67. doi: 10.1093/nar/gkp215

Table 4.

Exonic mutations known to result in exon skipping through ESE inactivation or ESS activation

Gene	Mutation	Ref.	Motif	Ref Seq	HSF prediction
ACADM	c.362C>T	(65)	−ESE (SF2/ASF)	ENST00000370841	−9G8ⁱ (357_362)
					−SF2/ASF^e (358_364)
					+EIE^h (359_364)
					−SRp40^e (359_365)
					− EIE^h (360_365)
					+IIE^c × 4 (359_367)
BRCA1	c.5080G>T	(64)	?	ENST00000357654	−EIE^h (5075_5080)
					+SRp55^e (5076_5081)
					−9G8ⁱ (5077_5082)
					−SF2/ASF^e (5078_5085)
					−IIE^c (5078_5083)
					+IIE^c (5079_5084)
					−ESS^a(5076_5083)
					+hnRNPA1^d (5080_5085)
BRCA2	c.8165C>G	(62)	−ESE	ENST00000380152	−SRp40^e (8162_8168)
					−ESE^f (8163_8168)
					+ESE^f × 2 (8164_8170)
					−SRp55^e (8163_8169)
					−SF2/ASF^e (8165_8171)
					−EIE^h × 4 (8160_8168)
BRCA2	c.5081G>T	(64)	?	ENST00000380152	+SC35^e (5075_5082)
					+SRp40^e (5080_5086)
					−ESE^f,h × 2 (5080_5086)
					−9G8ⁱ (5081_5086)
					−ESS^a (5078_5085)
DMD	c.4250T>A	(61)	+ESS (hnRNPA1)	ENST00000357033	+9G8ⁱ × 2 (4246_4251)(4248_4253)
					−EIE^h (4248_4253)
					+ESE^f (4250_4255)
					−IIE^c × 3 (4246_4253)
					+hnRNPA1^d (4249_4254)
MLH1	c.544A>G	(59)	?	ENST00000231790	+ESS^a (537_545)
					5′ss ΔCV = −6.30
MLH1	c.793C>T	(58)	?	ENST00000231790	+ESS^a (795_802)
MLH1	c.794G>A	(58)	?	ENST00000231790	−SRp40^e (793_799)
					−SC35^e (794_801)
					+ESS^c (794_799)
MLH1	c.882C>T	(58)	?	ENST00000231790	+SC35^e (876_883)
					−SRp55^e (877_882)
MLH1	c.988_990del	(58)	?	ENST00000231790	+SF2/ASF^e (983_989)
					−SRp55^e (985_990)
					+9G8ⁱ (985_990)
					−ESS^a (985_992)
MSH2	c.815C>T	(58)	?	ENST00000233146	−SRp55^e (813_818)
					+ESS^a (813_820)
					+ESS^c × 5 (801_819)
MSH2	c.274_276del	(58)	?	ENST00000233146	+SC35^e (272_279)
					+SRp40^e × 2 (274_285)
					−IIE^c × 2 (274_280)
LAMA2	c.2230C>T	(60)	?	ENST00000354729	−SF2/ASF^e (2226_2232)
					+ESS^c (2228_2235)
					+IIE^c × 2 (2229_2235)
					+ESS^a (2230_2237)
NF1	c.557A>T	(66)	−ESE	ENST00000356175	−SRp55^e (552_557)
					−ESE^f (552_557)
					−EIE^h × 4 (552_560)
					−9G8ⁱ (553_558)
					+ESS^a × 2 (550_557) (555_562)
NF1	c.910C>T	(66)	−ESE	ENST00000356175	−9G8ⁱ (905_910)
					−EIE^h (905_910)
					+ESE^f (908_913)
					−ESE^f (910_915)
					−ESS^a (906_913)
NF1	c.943C>T	(66)	−ESE	ENST00000356175	−SC35^e (941_948)
					−SF2/ASF^e (943_949)
					−PESE^g (942_949)
					−9G8ⁱ (938_943)
					+hnRNPA1^d (943_948)
					+IIE^c (942_947)
NF1	c.1007G>A	(66)	−ESE	ENST00000356175	+PESE^g (1007_1014)
					−EIE^h × 2 (1003_1011)
					+9G8ⁱ (1006_1011)
					+ESE^f (1007_1014)
					−ESS^a × 2 (1003_1011)
					−IIE^c × 4 (1003_1011)
					+hnRNPA1^d (1006_1011)
NF1	c.5719G>T	(66)	−ESE	ENST00000356175	−ESE^f × 5 (5715_5724)
					−EIE^h × 5 (5715_5724)
					−ESS^a × 2 (5714_5725)
					+PESS^g × 2 (5712_5720)
					+hnRNPA1^d (5719_5724)
NF1	c.6792C>A	(66)	−ESE	ENST00000356175	+ESE^f × 5 (6792_6797)
					−EIE^h × 2 (6788_6793) (6790_6795)
					+Tra2−βⁱ (6791_6795)
					−ESS^a × 2 (6787_6794) (6792_6799)
NF1	c.6792C>G	(66)	−ESE	ENST00000356175	+ESE^f (6792_6797)
					−EIE^h × 2 (6788_6793) (6790_6795)
					s+Tra2−βⁱ (6791_6795)
					−ESS^a × 2 (6787_6794) (6792_6799)
					+hnRNPA1^d (6790_6795)

+: a new site was created by the mutation; −: the motif was abolished by the mutation. Algorithms and matrices used to identify the motifs were:

^aSilencer motifs from Sironi et al. (31).

^bPESS octamers (28).

^cIIEs (30).

^dhnRNP motifs from HSF.

^eESE Finder matrices (19).

^fRESCUE ESE hexamers (63).

^gPESE octamers (28).

^hEIEs (30).

ⁱESE motifs from HSF. When multiple adjacent sites were predicted, the number of sites is indicated: ×5 means that five adjacent sites were modified by the mutation. Nucleotide numbering reflects the reference cDNA sequence with +1 corresponding to the A of the ATG translation initiation codon.